[Chimera-users] Surfaces

Hi Hernando, Dave, et al.
Those messages are common and expected. Although the error messages
themselves are new, the success rate in surface calculation is
actually improved from previous versions.
Surface calculation failures in MSMS on some proportion of structures
are a known and long-standing problem, possibly the most commonly
reported problem. We have been working for some time to write our
own code to replace MSMS, but it is not yet ready for public
consumption.
Changes in this most recent release separated the MSMS part from the
rest of Chimera (so it wouldn't crash Chimera), fixed at least one
bug in the MSMS library, and increased messages and fallback
procedures. In our tests this significantly decreased failures,
prevented crashes, and allowed calculation of some components when
some other components failed. By components I mean disconnected
blobs or pieces. Now I frequently see those messages but still get
the desired main/outer surface, whereas the component that failed was
a small internal cavity. There will still be instances of complete
MSMS failures, where you do not get any surface, but in our tests
much fewer than before.
> see "Surfaces" and "Major Bugs Fixed" in the release notes:
>http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html
MSMS will still fail on some structures, and we are still working on
replacement code.
I cannot easily explain cases of where you get a surface successfully
in the old version but not the new, but it is a numerical failure and
it is possible if anything about the computing environment changed
(sometimes even the position of the molecule!). The error messages
are new, however, so might be alerting you to failures on minor
components (small internal bubbles) that you might have been
blissfully unaware of in earlier versions.
Best,
Elaine
-----
Elaine C. Meng, Ph.D. meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
http://www.cgl.ucsf.edu/home/meng/index.html
On Aug 15, 2008, at 9:28 AM, David Konerding wrote:
>>> C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 1
> Calculation of some surface components failed (code 5).
> Falling back to single-component calculation.
> C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0
> Surface calculation failed, mscalc returned code 5
>> Two pdb files that I've been having problems with are 1JFF and 2P4N.
>> I see this error frequently myself - for example, 1ffk on Windows
> XP with Chimera
> build 2450.
>> Dave
>